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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaaaccatatccccttttttcgctaagcag

Basic information

species Oryza sativa
transcript LOC_Os03g49150.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G832740_T01 (Zea mays), 5'ss of exon 4
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcat----atattgc---------tttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgc----ttgcccttgtattactctggaattc----aaaaccatatcccctt--------ttttcgctaagcag
|| || |||||||||||| ||||||| ||||||||||| || |||||| | ||||||| ||   |  ||| |  |     | |||          |||| | | ||||   |||   |    | |      | |||  | |   ||     ||    | |  | |  ||||   ||  | ||      || || |  | ||         |||   || |||||
GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAGgtgatggccgcaacattgtcatggttttgtcgccttggatttgttctttttcccaaagaaatgtcctctgttcaaacagatctgtaactcggtttgcagattggtgcatcgattatattgttaatctggtggaatcagactcactgcaacaagatttgtcctgagcag

upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G856436_T02 (Zea mays), 5'ss of exon 4
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaa-accatatccccttttttcgctaagcag
|| ||||| ||||||||||||||||| ||||||||||| || |||||| | ||||||| ||   |  |||                || ||||  ||||  | ||   | |||   |  || ||    ||||  |           |  ||||| ||||||||| |   || | |     |||  |  ||||||||
GAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacgcaac---------------actctgttcaaacagac-ctgtgacttagtttgcaaaagac-cgcattgaata--------tattattattctggaattgactcactagaggaaatttgatt-ctaagcag

upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G856436_T01 (Zea mays), 5'ss of exon 1
--------------------------------------------GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaa-accatatccccttttttcgctaagcag
                                            || ||||| ||||||||||||||||| ||||||||||| || |||||| | ||||||| ||   |  |||                || ||||  ||||  | ||   | |||   |  || ||    ||||  |           |  ||||| ||||||||| |   || | |     |||  |  ||||||||
CGTATATTGCCTTGCATCTATGTTTTTATGATGCTCTTCTCTAGGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacgcaac---------------actctgttcaaacagac-ctgtgacttagtttgcaaaagac-cgcattgaata--------tattattattctggaattgactcactagaggaaatttgatt-ctaagcag

upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ14674 (Selaginella moellendorffii), 5'ss of exon 4
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaaaccatatccccttttttcgctaagcag
|||   || ||  | |||  ||||| ||||||||||||||| || |||||||||||||||    | | |    || | ||| | ||       ||||  | ||      |||      |                                                                            
GAATTCGCGCAGCACAAGGCCCAGAAGTACAAGGAAGGGAAGTTCATTTTAGAGAGgtaaatgccgtcattcaatgttttg-tatgtgaca--tcaaggatcttgctcgtttgtttgcag---------------------------------------------------------------------------

upper sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ26336 (Selaginella moellendorffii), 5'ss of exon 4
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgc-tgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaaaccatatccccttttttcgctaagcag
|||   || ||  | |||  ||||| ||||||||||||||| || |||||||||||||||      |  | ||||  | || ||||  ||||  ||||  |  |||      |    ||  ||                                                                         
GAATTCGCGCAGCACAAGGCCCAGAAGTACAAGGAAGGGAAGTTCATTTTAGAGAGgtaaa-----tgccgtcattcaatgttttgtatgtgcatcaaggatttcttgctcgtttgcttgcag-------------------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88844230|gb|CI005603.1|CI005603
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCAATACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88255532|gb|CI354356.1|CI354356
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88240560|gb|CI239722.1|CI239722
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|86825997|gb|CI362437.1|CI362437
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88376195|gb|CI533097.1|CI533097
EST:     GAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCAGTACTTTGTTACACATGATGC
genomic: GAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88662659|gb|CI471762.1|CI471762
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88366932|gb|CI553822.1|CI553822
EST:     AGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: AGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|9865632|gb|AU101382.1|AU101382
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|86884896|gb|CI314472.1|CI314472
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|86832532|gb|CI344782.1|CI344782
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|86886993|gb|CI324414.1|CI324414
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88663907|gb|CI488106.1|CI488106
EST:     ATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: ATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88437358|gb|CI528717.1|CI528717
EST:     CCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: CCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|218479417|gb|FG947989.1|FG947989
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTATAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|33691799|gb|CF320038.1|CF320038
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88535486|gb|CI464290.1|CI464290
EST:     AGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: AGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|86419787|gb|CI054588.1|CI054588
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|8858378|gb|AU095696.1|AU095696
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|58662158|gb|CK050838.1|CK050838
EST:     ACATGAGAAGAGCCAGAGGTACAAGGGAAGGGAAATTTATTTTAGCAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATG
genomic: ACATGAGAAGAGCCAGAGGTACAA-GGAAGGGAAATTTATTTTAG-AGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATG
EST: gi|22305231|gb|BQ906453.1|BQ906453
EST:     ACCATGAGAAGAGCCAGAGGTACCAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACCATGATG
genomic: A-CATGAGAAGAGCCAGAGGTA-CAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACA-CATGATG
EST: gi|88205477|gb|CI205326.1|CI205326
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88661066|gb|CI449874.1|CI449874
EST:     TGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: TGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|87013174|gb|CI281688.1|CI281688
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|87023464|gb|CI284611.1|CI284611
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|58663165|gb|CK051851.1|CK051851
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|86417196|gb|CI031405.1|CI031405
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|58657770|gb|CK046450.1|CK046450
EST:     GGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88526066|gb|CI453109.1|CI453109
EST:     GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: GCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88286375|gb|CI524874.1|CI524874
EST:     AGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: AGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88251691|gb|CI350119.1|CI350119
EST:     CACATGAGAAGAGCCAGAGGTACAAGGAAGGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: CACATGAGAAGAGCCAGAGGTACAAGGAA-GGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
EST: gi|88522677|gb|CI449508.1|CI449508
EST:     CATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG                         GTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC
genomic: CATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 56 (upstream exon), 75 (downstream exon)
Score: 72

GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctct ... cgctaagcagGTATAAGGTGTCTGGTCCTGATGGCAGCCACTACTTTGTTACACATGATGCTCATGTTGGGGGAAGCGACGTGGACGACGTATGAAGCACAACTCGACAT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAGgtaatcctcttaacctcatatattgctttgctgtgtttcaacaagctctacaatttaacattaaagagttatgcatcaagccgcttgcccttgtattactctggaattcaaaaccatatccccttttttcgctaagcag

- - - - - - - - - - - - - - - AAGGAA